This may come from hierarchical processing of the layout database. If the cell is listed as an hcell, those kinds of changes shouldn't happen to the cell. Is it already listed as an hcell or could you experiment by adding it to the hcell list to see if the nuisance warning goes away?

I know newer versions have minor changes to the way shapes can be manipulated through the hierarchy for the hcells. I can't be sure it will solve it but if not too troublesome you could try the newest version of Calibre (currently 2012.1). I found a TechNote that was written back in 2009 and it mentions there was no workaround back then. http://supportnet.mentor.com/reference/technotes/public/technote.cfm?tn=MG250430

Not sure I understand the question but I'm interested to discuss it more. Text labels in the layout (on layers that are listed in TEXT LAYER statements in the rule file) are usually attached to metal shapes in the layout, so that the nets containing those shapes can be named. The text in a cell would be used in that cell, along with metal in that cell. Once in awhile there will be a text in a cell, but the metal for that text will be promoted out of the cell, and the text will still be there, but now the metal isn't there in the cell to attach with the text label. This can cause a nuisance warning of unattached label.